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Immediately prior to European settlement the area had a violent history, due mainly to the presence of the great Māori warrior leader Te Rauparaha, whose pa was on nearby Kapiti Island. He died in 1849, the same year that a road connecting Paekakariki with Porirua was completed.

The name was spelt Paikakariki prior to 1905.[2]Paikakariki: A Sonnett is the title of an 1867 poem by William Golder.[3]

Paekakariki's history has been intimately linked with the railway, and there is a museum at the railway station commemorating this heritage. In 1886 the Wellington and Manawatu Railway Company's line from Wellington to Longburn was completed, and Paekakariki became an important stop on the journey. In 1908, the line was incorporated into the national network of the New Zealand Railways Department and became part of the North Island Main Trunk linking Wellington and Auckland, the North Island's most important line. In 1917, NZR withdrew dining cars from its passenger trains due to World War I economic difficulties and Paekakariki became a main refreshment stop on the trip north; originally a temporary measure, the dining cars did not return for decades and Paekakariki's status remained until the 1960s.

The locomotive depot gradually declined in importance due to changing motive power, and nowadays only EM classelectric multiple units are stabled here. The old steam locomotive depot is now the location of "The Engine Shed", the base of Steam Incorporated, one of New Zealand's premier railway preservation societies. The Paekakariki Station Precinct Trust has been established to manage the station area, including the museum and Steam Incorporated's depot, and firmly establish it as a historical and tourist attraction.

A notable historic building is the former restaurant 'The 1906', currently unoccupied, pending demolition to make way for a change in the motorway.

During the Second World War Paekakariki served as a major base for US Marines fighting in the Pacific Campaign. There were three main camps, all situated in or adjacent to present-day Queen Elizabeth Park. At the height of the occupation there were over 20,000 Americans stationed in the region, significantly outnumbering locals. The camps were used for training purposes, as well as rest and recreation for those returning from the Pacific combat zone. Paekakariki's steep surrounding hills proved suitable terrain for marching and mortar practice, whilst its beaches were used to stage amphibian invasions. They were the scene of an unfortunate tragedy in June 1943 when a landing craft was swamped by a wave during a nighttime training exercise. Nine men drowned in the heavy surf according to official figures; local rumor put the toll higher. The incident was never reported at the time due to wartime censorship provisions.[4][5]

While the American base in Paekakariki was only in existence for a few years it had an important and lingering impact on the region.[6] Several local place names remain as reminders of this wartime presence. Tarawa Street, for example, commemorates one of the bloodiest battles of the Pacific War which locally based marines fought in directly after the camps were abandoned in October 1943.